Interpretive Summary: Animal production systems in the US produce over 30 million tons of manure annually. There is an opportunity to increase the amount of manure being used as fertilizer, which could reduce costs for growers and also contribute to improved management of animal waste products. Nitrification is the process of breaking down manure and converting ammonium to nitrate, which can be used by plants. Nitrification is influenced by many factors, including physical properties of the soil and the relative abundance of soil bacteria that process nitrogen. Two different types of soil bacteria, AOA and AOB, are required for processing nitrogen from manure. The objective of this research was to examine how rates of nitrification and soil bacteria populations were affected by applying manure to several field sites that had different soil properties. It is extremely difficult to actually grow the bacteria responsible for nitrification, so we extracted DNA from soil and measured the amount of genes present in the soil that were specific to either AOB or AOA types. We found the ability of a soil to promote nitrification was positively correlated with the total amount of carbon and nitrogen present in the soil, whether or not manure was added to the soil. The quantity and type of clay minerals present in a soil also affected nitrification rates and bacterial populations. The number of AOA genes detected tended to be 10 times less than the number of AOB genes. Our research suggests AOA and AOB populations inhabit the same soil but have different optimum environmental conditions that are partly determined by the interaction between manure and soil properties. These results will help us determine which soils can most efficiently process manure, which will reduce grower costs and improve the sustainability of animal production systems in the US.

Technical Abstract:
Soil biotic and abiotic factors strongly influence nitrogen (N) availability and increases in nitrification rates associated with the application of manure. In this study, we examine the effects of edaphic properties and a dairy (Bos taurus) slurry amendment on N availability, nitrification rates and nitrifier communities. Soils of variable texture and clay mineralogy were collected from six USDA-ARS research sites and incubated for 28 d with and without dairy slurry applied at a rate of ~300 kg N ha-1. Periodically, sub-samples were removed for analyses of 2 M KCl extractable N and nitrification potential, as well as gene copy numbers of ammonia oxidizing bacteria (AOB) and archaea (AOA). Spearman coefficients for nitrification potentials and AOB copy number were positively correlated with total soil C, total soil N, cation exchange capacity (CEC), and clay mineralogy in treatments with and without slurry application. Our data show that the quantity and type of clay minerals present in a soil affect nitrifier populations, nitrification rates and the release of inorganic N. Nitrogen mineralization, nitrification potentials and edaphic properties were positively correlated with AOB gene copy numbers. On average, AOA gene copy numbers were an order of magnitude lower than those of AOB across the six soils and did not increase with slurry application. Our research suggests that the two nitrifier communities overlap but have different optimum environmental conditions for growth and activity that are partly determined by the interaction of manure derived ammonium with soil properties.